I solved this in the end by downloading the neokobe collection (all 90gb for the SECOND TIME) and making CHD's with an old version of Chdman.
Nostre, how are you launching thegames? I have a 'proper' chd with the disk name 'Galaxy Force II" and then one dummy chd with the name of the entry in fmtowns_cd.xml - something like gforce2. All games will launch from the dummy chd. Now i've successfully rebuilt mess i'm not sure the check sums need to match.
So far i've found:
Galaxy force and Genocide, pu-ra-li-ra panic bomber man and Afterburner 3 are both extremely playable with decent sound
4d sports, Chase HQ, Turbo Outrun and Flashback play but with compromised sound.